Sequence-tagged-site (STS) markers of arbitrary genes: the amount and nature of variation revealed in Norway spruce

We examined the amount and nature of variation revealed by cDNA-based seque nce-tagged-site (STS) markers in Norway spruce (Picea abies (L.) Karst.) us ing 39 pairs of heterologous primers that were based upon arbitrary genes i n black spruce (Picea mariana (Mill.) B.S.P.). A panel of 22 diverse Norway spruce genotypes was screened for variation that could be observed directl y using standard agarose gel electrophoresis, without additional manipulati on of amplification products. Examination of marker segregation among haplo id megagametophytes revealed that nine markers behaved in a codominant mann er, two markers had codominant length polymorphisms and null alleles, and f our others had dominant length polymorphisms. DNA sequencing of codominant alleles at seven loci indicated that most insertions/deletions (indels) wer e in noncoding regions and that alleles often differed by the presence or a bsence of direct repeats that ranged in size from three to 23 bp. The nine markers that showed exclusively codominant polymorphisms in Norway spruce h ad an average observed heterozygosity of 0.30 and an average of 2.9 alleles in the panel of 22 trees. These levels of variation are similar to those p reviously found for similar sets of markers in other spruces, and appear to be at least as high as those revealed by polymorphic allozyme markers in N orway spruce. Polymorphisms at one STS locus suggested a higher affinity be tween Norway spruce and white spruce (Picea glauca (Moench) Voss) than betw een either of these spruces and black spruce. The STS markers described in this report should be useful in a variety of applications in Norway spruce, including population studies and genome mapping.